Preparation of tissue sections using fluorescence-based detection

ABSTRACT

The present disclosure is directed to an improved method for distinguishing tissue from an embedding medium, such as paraffin in a formalin-fixed paraffin-embedded sample. The method involves the use of fluorescence of naturally-occurring species in tissue to determine the location of the tissue in the embedded sample. An embedded sample is generally excited by light of a selected wavelength, and the fluorescence emission at an emitted wavelength is used to locate the boundary or location of the tissue in the embedded sample.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.62/537,848, filed Jul. 27, 2017, the contents of which are incorporatedby reference in their entirety.

FIELD OF THE INVENTION

The present disclosure relates to methods of preparing tissue sectionsfrom an embedded sample such as a formalin-fixed paraffin-embeddedsample using fluorescence-based detection.

BACKGROUND

The formation of a formalin-fixed paraffin-embedded (FFPE) tissue blockserves to preserve the morphology and cellular content of a tissuesample. Tissue processing generally involves placing an isolated tissuein formalin for a time period such as a few days, and then embedding thetissue in a paraffin wax. FFPE samples can be conveniently stored atroom temperature for extended periods of time, and are especially usefulfor immunohistochemical staining and morphology analyses. FFPE samplesmay also be used for profiling gene expression and studying diseases.

At the time of biological testing, the FFPE tissue block is generallytrimmed by cutting the tissue block on a microtome. The tissue block maybe analyzed to determine the boundaries of the tissue in the FFPE by atechnician or using an automated method. In the former case, atechnician generally examines the FFPE block to observe the diffuseimage of the tissue embedded in the paraffin. The technician mayascertain what the cross-sectional area of a section comprising thetissue should look like and compare that to the tissue sections as theyemerge from the microtome blade. Preferably, the tissue block is trimmedto expose a representative amount of tissue to the surface of the blockand to ensure that the block face is in line with the knife's edge.

During automated analysis, a camera is commonly utilized to image thetissue. A light source illuminates the surface of the tissue block at anangle to distinguish the difference between the paraffin and tissuesurfaces. Since paraffin is comparably smoother than tissue, automatedanalysis utilizes the different natural textures of paraffin and tissueto differentiate between the two materials.

US 2010/0118133 A1 discloses an automated method and device forproducing thin sections of tissue and obtaining an image of a surfacegenerated by sectioning the sample using a camera. A device is used toevaluate the image to determine whether the section of the sample isacceptable for further use.

Many existing methods provide inaccurate and inconsistent data when usedto analyze different tissue and paraffin types, since many methods aresensitive to variability of optical and surface characteristics oftissue and paraffin. In some cases, it is quite difficult to distinguishtissue from paraffin in an FFPE sample using existing methods.

Accordingly, there is a need for an additional method and apparatus fordetermining the location of a tissue sample in an embedding medium suchas paraffin. The present methods and apparatus provide an accurate andconsistent method for differentiating tissue from paraffin in a tissueblock.

SUMMARY OF THE INVENTION

In an embodiment, the present disclosure provides a method ofdetermining the location of a tissue in an embedded sample. The methodcomprises irradiating an embedded sample with light having a wavelengthof from about 200 nm to about 600 nm, wherein the embedded samplecomprises a tissue and an embedding medium; detecting fluorescenceemission of the embedded sample; and determining the location of atleast a portion of the tissue in the embedded sample based on thefluorescence emission.

In another embodiment, the present disclosure provides a method ofdetermining the location of a tissue in an embedded sample. The methodcomprises irradiating an embedded sample comprising a tissue and anembedding medium with at least one light source to produce a firstfluorescence emission and a second fluorescence emission; detecting thefirst fluorescence emission and the second fluorescence emission; anddetermining the location of at least a portion of the tissue in theembedded sample based on the first fluorescence emission and the secondfluorescence emission.

In another embodiment, the disclosure provides an apparatus for slicinga tissue section from an embedded sample. The apparatus comprises amicrotome comprising a sample holder adapted for linear motion, a knifeholder and a knife held by the knife holder opposite the sample holder,such that when the sample holder is moved linearly, a sample held by thesample holder is sliced by the knife to form a tissue section; at leastone light source directed at the sample holder; and an optical systempositioned to capture emitted light from a sample held by the sampleholder.

These and other features and advantages of the present methods andapparatus will be apparent from the following detailed description, inconjunction with the appended claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The present teachings are best understood from the following detaileddescription when read with the accompanying drawing figures. Thefeatures are not necessarily drawn to scale.

FIGS. 1A and 1B show photographs of a tissue sample that is fullyembedded in paraffin (FIG. 1A) and a tissue sample that is embedded inparaffin and trimmed to expose a section of the tissue (FIG. 1B).

FIG. 2 shows a photograph that displays an example of a tissue in aformalin-fixed paraffin-embedded block where the tissue isindistinguishable from paraffin in the block sample.

FIGS. 3A and 3B show an image of the interface between a tissue andparaffin in a formalin-fixed paraffin-embedded tissue block using brightfield analysis (FIG. 3A) and dark field analysis (FIG. 3B).

FIGS. 4A and 4B show graphs of the excitation spectra (FIG. 4A) and theemission spectra (FIG. 4B) of various fluorophores endogenous to humantissue. Each graph shows the wavelength of light versus fluorescenceintensity.

FIG. 5 shows a collection of fluorescent images of the fluorescenceemission of block faces of a formalin-fixed paraffin-embedded block at4× magnification. The images were obtained by imaging fluorescence ofthe formalin-fixed paraffin-embedded tissue block sample in betweenslices.

FIG. 6 is a graph displaying the pixel intensity of images ofautofluorescence of elastin and collagen in a formalin-fixedparaffin-embedded tissue block after each cut of a section from thetissue block.

FIGS. 7A-7D show hardware diagrams for fluorescence-based imagingsystems in accordance with embodiments of the present disclosure.

FIG. 8A is a collection of fluorescence emission images of variousslices of a formalin-fixed paraffin-embedded tissue block samplecomprising a single tissue. The images were obtained using a 365 nmexcitation source with a 560 nm 55 nm bandpass emission filter.

FIG. 8B is a collection of fluorescence emission images of the same FFPEslices, obtained using a 280 nm excitation source and 405 nm 20 nm widebandpass emission filter.

DEFINED TERMINOLOGY

It is to be understood that the terminology used herein is for purposesof describing particular embodiments only, and is not intended to belimiting. The defined terms are in addition to the technical andscientific meanings of the defined terms as commonly understood andaccepted in the technical field of the present teachings.

The term “autofluorescence” refers to the natural emission of light by abiological molecule such as a protein.

The term “fluorophore” refers to a fluorescent compound that can re-emitlight upon excitation with light. The term “endogenous fluorophore”refers to a naturally-occurring biological substance capable ofautofluorescence.

A “fixed” tissue is one that has been contacted with a fixing agent fora suitable period of time.

An “embedded tissue” or “embedded sample” is a tissue sample that ispartially or completely surrounded by an embedding medium such as aparaffin or an epoxy resin. The embedded tissue or embedded sample ofthe present disclosure should not be confused with a tissue section thatresults from slicing or trimming of an embedded tissue.

The term “formalin-fixed paraffin-embedded block” or “formalin-fixedparaffin-embedded sample” or “FFPE sample” refers to a formalin-treatedtissue embedded in paraffin.

The terms “pixel intensity” or “pixel intensity values” are usedinterchangeably and refer to the detected fluorescent signal averagedover a region of interest in a digital image. During acquisition of adigital image, the photons that are detected at each pixel are convertedto an intensity value that is proportional to the number of detectedphotons. The pixel intensity can be used to determine the localconcentration of fluorophores in a specimen.

As used in the specification and appended claims, and in addition totheir ordinary meanings, the terms “substantial” or “substantially” meanto within acceptable limits or degree to one having ordinary skill inthe art. For example, “substantially cancelled” means that one skilledin the art considers the cancellation to be acceptable.

As used in the specification and the appended claims and in addition toits ordinary meaning, the terms “approximately” and “about” mean towithin an acceptable limit or amount to one having ordinary skill in theart. The term “about” generally refers to plus or minus 15% of theindicated number. For example, “about 10” may indicate a range of 8.5 to11.5. For example, “approximately the same” means that one of ordinaryskill in the art considers the items being compared to be the same.

In the present disclosure, numeric ranges are inclusive of the numbersdefining the range. In the present disclosure, wherever the word“comprising” is found, it is contemplated that the words “consistingessentially of” or “consisting of” may be used in its place.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by those working in thefields to which this disclosure pertain.

DETAILED DESCRIPTION

Methods are provided which allow for one to distinguish a tissue from anembedding medium in an embedded sample. FIG. 1 shows a tissue fullyembedded in paraffin (1A) and a corresponding trimmed sample (1B). Inorder to determine the location of a tissue for trimming, tissue in anembedding medium is often visually assessed to identify the interfacebetween the tissue and the embedding medium. In many cases, it isdifficult to visually identify the interface between the tissue andembedding medium. Such an example is shown in FIG. 2, where the tissuein an FFPE sample is indistinguishable from the paraffin embeddingmedium. FIGS. 3A and 3B show an image of the interface between a tissueand paraffin in a formalin-fixed paraffin-embedded tissue block obtainedusing bright field analysis (FIG. 3A) and dark field analysis (FIG. 3B).In some cases, it may be difficult to identify the interface between atissue and an embedding medium using such methods. The present methodand apparatus solves this problem, using fluorescence to locate tissuein an embedded sample.

Contrary to existing methods, the present methods utilizeautofluorescence of endogenous fluorophores in tissue to distinguishtissue from an embedding medium such as paraffin or an epoxy resin.Contrasting between tissue and an embedding medium can be achieved byirradiating an embedded sample such as a formalin-fixedparaffin-embedded (FFPE) tissue block at an appropriate wavelength, anddetecting the resulting fluorescence emission. The fluorescence emissioncan be used to determine the location of at least a portion of thetissue. For example, the present methods can be used to locate thesurface of tissue in a formalin-fixed paraffin-embedded (FFPE) tissueblock. After the tissue is located in the embedded sample, the tissuemay be further processed by trimming or slicing to obtain one or moretissue sections. The fluorescence methods of the present disclosure areperformed prior to biological analysis or staining of a tissue section.The present methods are effective for a wide-variety of tissue types,and can be used to distinguish tissue from paraffin in cases where thetissue is optically indistinguishable from the embedding medium undernormal lighting conditions.

Fluorescence, which is the emission of light by a substance that hasabsorbed electromagnetic radiation, is commonly used to elucidate thepresence or amount of an analyte. Fluorescent compounds are capable ofabsorbing and emitting light under certain conditions, where the emittedlight is generally of lower energy. Autofluorescence is natural emissionof light by biological molecules, generally at a wavelength peak orpattern, when the molecules are irradiated at certain wavelengths. Eachfluorescent biological molecule has its own excitation and emissionspectrum. In human and animal tissue, proteins such as collagen andelastin are capable of autofluorescence. FIG. 4A shows the excitationspectra of a number of biological molecules, and FIG. 4B shows theemission spectra of the same biological molecules. Proteins can serve asendogenous fluorophores and can be detected or tracked by monitoring theprotein's fluorescence emission.

In an embodiment, the present disclosure provides a method ofdetermining the location of a tissue in an embedded sample. The methodcomprises irradiating an embedded sample with light having a wavelengthof, for example, from about 200 nm to about 600 nm, wherein the embeddedsample comprises a tissue and an embedding medium; detectingfluorescence emission of the embedded sample; and determining thelocation of at least a portion of the tissue in the embedded samplebased on the fluorescence emission.

In some embodiments, the embedding medium is paraffin. In someembodiments, the embedding medium is an epoxy resin.

In some embodiments, the fluorescence emission is detected using animaging device. In some embodiments, the imaging device comprises acamera such as a digital camera. In such cases, an embedded samplecomprising tissue and an embedding medium such as paraffin is irradiatedwith light and the resulting fluorescence emission is captured using adigital camera. The presence of fluorescence in the digital imageprovides an indication that tissue is present in the sample under study.In some embodiments, the present method is performed using an opticalsystem comprising a digital camera and a microtome. In some embodiments,the present method is performed using a fluorescence microscope.

In some embodiments, the embedding medium exhibits no substantialfluorescence when irradiated at a chosen wavelength.

The present methods may be used to analyze a tissue of any type. In someembodiments, the tissue is a human tissue. In some embodiments, thetissue is an animal tissue. In some embodiments, the tissue is a mouse,rat, dog, or primate tissue. The present method may be used to analyze atissue section from any organ or anatomical part. In some embodiments,the tissue is isolated from the breast, prostate, lung, colon, rectum,urinary bladder, uterine corpus, thyroid, kidney, oral cavity (e.g.,tonsil), pancreas, liver, cervix, stomach, small intestine, brain,spinal cord, heart, bone, joints, esophogus, gallbladder, adipose, skin,spleen, placenta, penis, urethra, fallopian tube, ovary, vulva, adrenalglands, appendix, or eye. In some embodiments, the tissue is pelletedcells from a human or an animal source. In some embodiments, the presentmethod is used to test a diseased or healthy tissue. In someembodiments, the present method is used to identify cancer, infectiousdisease, metabolic disease, degenerative disease, inflammatory disease,or a combination thereof.

In some embodiments, the embedded sample is a formalin-fixedparaffin-embedded sample. The formalin-fixed paraffin-embedded samplemay be formed from any type of paraffin. In some embodiments, theparaffin is a blend of fully refined paraffin wax and a synthetic resinor polymer. In some embodiments, the paraffin comprisesdimethylsulfoxide (DMSO). In some embodiments, the formalin-fixedparaffin-embedded sample is formed from granulated paraffin wax, fullyrefined paraffin wax, semi-refined paraffin wax, or a combinationthereof. Thus, in some embodiments, a tissue may be distinguished fromgranulated paraffin wax, fully refined paraffin wax, or semi-refinedparaffin wax in a formalin-fixed paraffin-embedded sample. In someembodiments, the formalin-fixed paraffin-embedded sample is formed fromSpectrum paraffin, Millipore paraffin, Fisherfinest Histopath paraffinwax, EMS Paramat, Paraplast, Polyfin, Sakura Finetek Tissue Tek VIP,Leica Surgipath Paraplast, or a combination thereof.

In some embodiments, the embedding medium is an epoxy resin. In someembodiments, the epoxy resin is a glycidyl epoxy resin. In someembodiments, the epoxy resin is a non-glycidyl epoxy resin. In someembodiments, the epoxy resin is a non-glycidyl resin selected from analiphatic and cyclo-aliphatic resin. In some embodiments, the epoxyresin is a glycidyl epoxy selected from glycidyl amine, glycidyl ester,glycidyl ether, and a combination thereof. In some embodiments, theepoxy resin is ethylene glycol diglycidyl ether. In some embodiments,the epoxy resin is Araldite, Quetol, Epon 812, Embed 812, Poly-Bed 812,or a combination thereof. In some embodiments, the epoxy resin is aglycerol-based aliphatic epoxy resin. In some embodiments, embedding atissue in an epoxy resin provides tissue sections having improvedmorphology.

In some embodiments, the embedded sample is cut or sliced to provide aslice and a trimmed block. In some embodiments, the embedded sample issliced or trimmed on a microtome. In some embodiments, theautofluorescence of an embedded sample is detected while the embeddedsample is being sliced or trimmed by a microtome. The trimmed block isirradiated with light, and analyzed to determine the presence offluorescence. Imaging may be used to determine the presence offluorescence. The trimming and/or irradiation process is repeated asneeded. For example, the trimming/irradiation process may be repeateduntil the surface of the tissue is found.

In some embodiments, autofluorescence of one or more endogenous speciesis measured quantitatively to determine the location of tissue in anembedded sample.

In some embodiments, pixel intensity of a fluorescence digital image isused to determine the location of a tissue in an embedded sample. Atrimmed block is irradiated with light, and a digital image is acquiredusing a fluorescence microscope. The fluorescence microscope systemcomprises software that converts photons detected during fluorescenceanalysis to pixel intensity values, allowing the user to determine thepixel intensity for a region of interest. The trimmed block may befurther sliced or trimmed and analyzed by the fluorescence microscopesystem to provide a second digital image. A comparison of the pixelintensity of two or more digital images can be used to determine thelocation of the tissue in the embedded sample. For example, an increasein pixel intensity values between two digital images can indicate thatthe tissue in the trimmed block is exposed and is ready to be cut andused for biological testing.

In some embodiments, the present method is used to determine thelocation of a surface of a tissue sample in an embedded sample. In someembodiments, the present method is used to determine the location of atissue-to-embedding medium transition or embedding medium-to-tissuetransition in an embedded sample. In some embodiments, the presentmethod is used to locate a tissue in its entirety.

In some embodiments, the method comprises slicing a section from theembedded sample and accepting or rejecting the section based on thedetermined location of the tissue surface. In some embodiments, theirradiating is performed multiple times and the embedded sample is cutprior to each irradiation.

The fluorescence emission of an endogenous species in tissue may be usedto determine the location of a tissue in an embedded sample. Anyendogenous fluorophore in tissue may be used. In some embodiments, theendogenous fluorophore is collagen, elastin, tryptophan, a porphyrin, aflavin, NADH, pyridoxin, a lipo-pigment, or a combination thereof. Insome embodiments, the fluorescence emission of collagen is used todetermine the location of a tissue in an embedded sample. In someembodiments, the fluorescence emission of elastin is used to determinethe location of a tissue in an embedded sample. In some embodiments, thefluorescence emission of tryptophan is used to determine the location ofa tissue in an embedded sample. In some embodiments, one or more ofcollagen, elastin, and tryptophan are used to determine the location ofa tissue in an embedded sample.

In some embodiments, an excitation light having a wavelength of fromabout 320 nm to about 380 nm is used to detect collagenautofluorescence. In some embodiments, collagen maximum fluorescenceemission is detected at a wavelength of from about 375 nm to about 425nm.

In some embodiments, an excitation light having a wavelength of fromabout 320 nm to about 380 nm is used to detect elastin autofluorescence.In some embodiments, elastin maximum fluorescence emission is detectedat a wavelength of from about 400 nm to about 450 nm.

In some embodiments, an excitation light having a wavelength of fromabout 180 nm to about 230 nm is used to detect tryptophanautofluorescence. In some embodiments, tryptophan maximum fluorescenceemission is detected at a wavelength of from about 300 nm to about 350nm.

The embedded sample may be irradiated with light having any suitablewavelength. In some embodiments, an embedded sample is irradiated withlight having a wavelength of from about 200 nm to about 600 nm. Thus, insome embodiments, an embedded sample is irradiated with light having awavelength of from about 200 nm to about 600 nm, from about 200 nm toabout 550 nm, from about 200 nm to about 500 nm, from about 200 nm toabout 450 nm, from about 200 nm to about 400 nm, from about 200 nm toabout 350 nm, from about 250 nm to about 600 nm, from about 250 nm toabout 550 nm, from about 250 nm to about 500 nm, from about 250 nm toabout 450 nm, from about 250 nm to about 400 nm, from about 300 nm toabout 500 nm, from about 300 nm to about 550 nm, from about 300 nm toabout 600 nm, from about 350 nm to about 600 nm, from about 400 nm toabout 600 nm, from about 450 nm to about 600 nm, from about 350 nm toabout 550 nm, from about 350 nm to about 500 nm, from about 400 nm toabout 600 nm, from about 400 nm to about 550 nm, or from about 450 nm toabout 600 nm.

The fluorescence emission of the embedded sample can be detected at anysuitable wavelength, usually the maximum emission wavelengths. In someembodiments, the embedded sample has a maximum fluorescence emission ata wavelength of from about 300 nm to about 600 nm. Thus, in someembodiments, the embedded sample has a maximum fluorescence emission ata wavelength of from about 300 nm to about 600 nm, from about 300 nm toabout 550 nm, from about 300 nm to about 500 nm, from about 300 nm toabout 450 nm, from about 300 nm to about 400 nm, from about 350 nm toabout 600 nm, from about 350 nm to about 550 nm, from about 350 nm toabout 500 nm, from about 350 nm to about 450 nm, from about 400 nm toabout 600 nm, from about 450 nm to about 550 nm, or from about 500 nm toabout 600 nm.

Fluorescence methods are generally performed using a light source and adetector configured to detect fluorescence as known in the art. In someembodiments, fluorescence techniques are carried out using a lightsource capable of shining light at a particular wavelength or rangethereof. In some embodiments, an embedded sample is irradiated using oneor more light sources. In some embodiments, the light source is alight-emitting diode (LED) light source. In some embodiments, the lightsource is a mercury arc lamp. In some embodiments, the light source is axenon arc lamp. In some embodiments, the light source is a LASER. Insome embodiments, the present method is performed using a fluorescencesystem having one or more excitation filters. In some embodiments, thefluorescence system comprises an aperture and one or more emissionfilters. In some embodiments, the fluorescence system comprises animaging lens and an imaging camera.

An embedded sample may be formed using any suitable method. In someembodiments, a tissue is obtained from a subject and sectioned. Thetissue is contacted with a formalin solution and fixed for at least 48hours at room temperature. The tissue is commonly dehydrated using aseries of ethanol baths and then embedded into a wax block. The waxgenerally comprises a mixture of straight chain alkanes having a chainlength of from about 20 to about 40 carbons. In some embodiments,glutaraldehyde is used as a fixative to embed a tissue in an epoxyresin. The embedded sample may be sliced or sectioned for any subsequentanalysis (e.g., microscopic slide analysis).

In some embodiments, the embedded sample may be further trimmed orsectioned to form a tissue section or slice. The embedded sample may betrimmed or sectioned using any suitable method (e.g., using a microtomeblade). In some embodiments, a clearing agent such as a xylene can beused to remove the embedding medium from the section. In someembodiments, the tissue section is stained using at least one stain suchas a Haematoxylin and/or Eosin, Acid/Basic Fuchsin, or Gram stain. Insome embodiments, the tissue section may be mounted onto a slide foranalysis. The stained tissue section may undergo further analysis usingany suitable method (e.g., pathological analysis using a microscope).

In some embodiments, the present methods are performed to locate anembedded tissue for use in a fluorescence in situ hybridization (FISH)testing method. In some embodiments, the present methods are performedto locate an embedded tissue for use in a chromogenic in situhybridization (CISH) testing method.

In another embodiment, the present disclosure provides a method ofdetermining the location of a tissue in an embedded sample byirradiating an embedded sample comprising a tissue and an embeddingmedium with at least one light source to produce a first fluorescenceemission and a second fluorescence emission; detecting the firstfluorescence emission and the second fluorescence emission; anddetermining the location of at least a portion of the tissue in theembedded sample based on the first fluorescence emission and the secondfluorescence emission.

In some embodiments, an embedded sample is irradiated with light havinga wavelength of from about 250 nm to about 325 nm. In some embodiments,an embedded sample is irradiated with light having a wavelength of fromabout 300 nm to about 400 nm. In some embodiments, an embedded sample isirradiated concurrently at both wavelengths. In some embodiments, brightfield microscopy is used in combination with the present method todetermine the location of the tissue in the embedded sample.

In some embodiments, a first fluorescence emission is generated byfluorescence of an embedding medium in the embedded sample (e.g.,paraffin). In some embodiments, a second fluorescence emission isgenerated by autofluorescence of a tissue component present in theembedded sample. In some embodiments, the first fluorescence emissionhas maximum fluorescence at a wavelength of from about 375 nm to about425 nm and the second fluorescence emission has maximum fluorescence ata wavelength of from about 500 nm to about 600 nm.

In some embodiments, the embedded sample is irradiated using two or morelight sources (e.g., two, three, four, five, or six). In someembodiments, the two or more light sources are the same. In someembodiments, the two or more light sources are different. In someembodiments, the sample is irradiated simultaneously or separately bythe two or more light sources.

In some embodiments, the method is performed in the absence of adichroic filter.

In some embodiments, the method comprises front illuminating an embeddedsample traversely, such as at an oblique angle of from about 10 degreesto about 20 degrees from a plane of a face of the embedded sample. Insome embodiments, a fluorescence emission is collected by a lens havinga high numerical aperture. In some embodiments, illumination from two ormore traverse directions (e.g., left or right or top or bottom) producesa uniform excitation and emission pattern.

In some embodiments, a high numerical aperture objective lens is usedfor excitation and collection of emitted light, as well as a filter cubewith a dichroic beam splitter with excitation and emission filters. Insome embodiments, an additional lens is used after the dichroic filterto focus the emitted light onto an imaging sensor.

In some embodiments, the embedding medium is weakly fluorescent. Thus,in some embodiments, a fluorescent dye can be added to the embeddingmedium. The fluorescent dye emits light at a different wavelength thanthe emission wavelength of an endogenous fluorophore in the tissuesample, thus a fluorescence emission from the fluorescent dye can beused to determine the location of tissue in an embedded sample. Thefluorescent dye may be incorporated into the embedding medium prior toformation of the embedded sample.

In another embodiment, the disclosure provides an apparatus for slicinga tissue section from an embedded sample. The apparatus comprises amicrotome comprising a sample holder adapted for linear motion, a knifeholder and a knife held by the knife holder opposite the sample holder,such that when the sample holder is moved linearly, a sample held by thesample holder is sliced by the knife to form a tissue section; at leastone light source directed at the sample holder; and an optical systempositioned to capture emitted light from a sample held by the sampleholder.

In some embodiments, the apparatus comprises at least two light sources.In some embodiments, the apparatus comprises at least three lightsources. In some embodiments, the apparatus comprises at least fourlight sources.

In some embodiments, the apparatus comprises a filter cube with adichroic beam splitter with excitation and emission filters. In someembodiments, the apparatus comprises a dichroic filter. In someembodiments, the apparatus comprises an additional lens after thedichroic filter to focus the emitted light onto an imaging sensor. Insome embodiments, the apparatus comprises an emission filter in a filtercube assembly, where switching of at least one excitation sourceswitches at least one filter.

In some embodiments, the apparatus includes one or more excitationfilters. In some embodiments, the apparatus comprises an aperture. Insome embodiments, the apparatus comprises a lens having a high numericalaperture. In some embodiments, the apparatus comprises one or moreemission filters. In some embodiments, the apparatus comprises animaging lens. In some embodiments, the optical system comprises acamera. In some embodiments, the optical system comprises a digitalcamera. In some embodiments, the optical system is capable of detectingat least one fluorescence emission.

In some embodiments, the apparatus comprises a microtome blade, at leastone light source, at least one excitation filter, at least one aperture,at least one emission filter, a lens assembly, and at least one camera.

In some embodiments, the apparatus comprises a microtome blade, at leasttwo light sources, at least two excitation filters, at least oneaperture, at least two emission filters, a lens assembly, at least onecamera, and at least one mechanism for switching between emissionfilters.

In some embodiments, the apparatus comprises a microtome blade, at leasttwo light sources, at least two excitation filters, at least oneaperture, a dual-band bandpass emission filter, a lens assembly, and atleast one multi-color camera. In some embodiments, the multicolor camerahas microfilters in front of each pixel.

In some embodiments, the apparatus comprises a microtome blade, at leastone light source, at least one excitation filter, at least one aperture,an objective lens assembly, a tube lens or relay lens, a dichroicbeamsplitter, at least one emission filter in filter cube assembly, atleast one camera. In some embodiments, switching between excitationsources is accompanied by switching filters.

FIGS. 7A-7D show non-limiting examples of fluorescence-based imagingsystems. Each system includes a microtome blade, one or more lightsources, one or more excitation filters, a 2-dimensional aperture, oneor more emission filters, an imaging lens, and an imaging camera. FIG.7A shows a single-color fluorescence imaging system 701 that can be usedto image an embedded sample 703 which comprises a microtome blade 705,an LED light source 707, an excitation filter 709, an aperture 711, anemission filter 713 with a mechanism for switching emission filters, alens assembly 715, and a camera 717 in accordance with an embodiment ofthe disclosure. FIG. 7B shows a two-color fluorescence imaging system719 that can be used to image an embedded sample 721 which comprises amicrotome blade 723, LED light sources 725, excitation filters 727,apertures 729, an emission filter with a motorized wheel assembly 731, alens assembly 733, and a camera 735 in accordance with an embodiment ofthe disclosure. FIG. 7C shows a two-color fluorescence imaging system737 that can be used to image an embedded sample 739 which comprises amicrotome blade 741, LED light sources 743, excitation filters 745,apertures 747, a two-color band-pass emission filter 749, a lensassembly 751, a color camera 753 having a multi-color image sensor 755in accordance with an embodiment of the disclosure. FIG. 7D shows afluorescence imaging system 757 which can be used to image an embeddedsample 759 which comprises a microtome blade 761, an LED light source763, an aperture 765, an excitation filter 767, an objective lensassembly 769, a dichroic beam splitter 771, an emission filter 773, atube lens or relay lens 775, and a camera 777 where switching of theexcitation source is accompanied by switching the filters in accordancewith an embodiment of the disclosure.

In some embodiments, the optical system comprises a processor incommunication with the optical system and configured to provide a signalbased on a fluorescence emission from the sample.

It is to be understood that the teachings of this disclosure are notlimited to the particular embodiments described, and as such can, ofcourse, vary. It is also to be understood that the terminology usedherein is for the purpose of describing particular embodiments only, andis not intended to be limiting, since the scope of the present teachingswill be limited only by the appended claims.

As disclosed herein, a number of ranges of values are provided. It isunderstood that each intervening value, to the tenth of the unit of thelower limit, unless the context clearly dictates otherwise, between theupper and lower limits of that range is also specifically disclosed.Each smaller range between any stated value or intervening value in astated range and any other stated or intervening value in that statedrange is encompassed within the invention. The upper and lower limits ofthese smaller ranges may independently be included or excluded in therange, and each range where either, neither, or both limits are includedin the smaller ranges is also encompassed within the invention, subjectto any specifically excluded limit in the stated range. Where the statedrange includes one or both of the limits, ranges excluding either orboth of those included limits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure belongs. Although any methods andmaterials similar or equivalent to those described herein can also beused in the practice or testing of the present teachings, some exemplarymethods and materials are now described.

All patents and publications referred to herein are expresslyincorporated by reference. The citation of any publication is for itsdisclosure prior to the filing date and should not be construed as anadmission that the present claims are not entitled to antedate suchpublication. Further, the dates of publication provided can be differentfrom the actual publication dates which can be independently confirmed.

As used in the specification and appended claims, the terms “a,” “an,”and “the” include both singular and plural referents, unless the contextclearly dictates otherwise.

As will be apparent to those of skill in the art upon reading thisdisclosure, each of the individual embodiments described and illustratedherein has discrete components and features which can be readilyseparated from or combined with the features of any of the other severalembodiments without departing from the scope or spirit of the presentteachings. Any recited method can be carried out in the order of eventsrecited or in any other order which is logically possible.

Example 1

This Example illustrates a method of measuring fluorescence ofendogenous fluorophores in human tissue in accordance with an embodimentof the present disclosure.

An FFPE human tissue block was obtained. The FFPE block was analyzed todetermine if autofluorescence can be used to differentiate tissue in theFFPE block from paraffin. The uncut FFPE block was subjected to lightcorresponding to the excitation wavelengths of elastin and collagen. Anyresulting fluorescence emission was detected using digital imaging. TheFFPE block was cut using a ThermoFisher microtome blade, whereconsecutive cuts of the FFPE block were performed in intervals rangingfrom 5 to 40 microns in thickness. After each cut, the block face of theFFPE block was subjected to light corresponding to the excitationwavelengths of elastin and collagen and the fluorescence emission wasdetected using digital imaging. The images were collected at a 4×magnification. The pixel intensity for each image was recorded andplotted.

For the experiment, an X-Cite 120 Q was used as the light source. Thefluorescence of elastin was detected using a Zeiss Filter Set 38 forfluorescein or green fluorescent protein (GFP) having anexcitation/emission spectra of 470/525 nm (bandpass of 40 nm). Thefluorescence of collagen was detected using a Zeiss Filter Set 49 forDAPI having an excitation/emission spectra of 365/445 nm (bandpass of 50nm). The exposure times for GFP and DAPI was 65 msec and 175 msec,respectively. A Zeiss Axio Imager M2 was used to visualize the presenceof autofluorescence in the FFPE sample. Images of autofluorescence wereobtained using an AxioCAM MRM.

The experimental images are shown in FIG. 5. A plot of cut number versusthe pixel intensity of each image was plotted, as shown in FIG. 6.

FIG. 5 shows that fluorescent imaging of a tissue in a FFPE block can beused to detect and locate the tissue in the FFPE block. Moreover, asshown in FIG. 6, there was an increase from 200 pixels for an uncut FFPEblock to over 1,000 pixels for the faced block when using both GFP andDAPI. Based on the results, it is believed that the observed increase inpixel intensity can be utilized to determine when the tissue is exposedand ready to be cut and used for biological testing.

Example 2

This Example illustrates a method of contrasting tissue usingfluorescence emission of paraffin in accordance with an embodiment ofthe disclosure.

A FFPE human tissue block was obtained. The FFPE block was analyzed todetermine if fluorescence of paraffin can be used to differentiatetissue in the FFPE block from paraffin. In particular, the experimentwas conducted to determine if an image could be obtained of paraffinfluorescence in the presence of the endogenous fluorophores in tissue.Fluorescence intensity of tissue in a FFPE sample was measured using a365 nm LED excitation source with an emission filter centered at 560 nm(55 nm bandpass). Fluorescence intensity of the paraffin surrounding thetissue in an FFPE sample was measured with a 280 nm LED excitationsource and an emission filter centered at 405 nm (20 nm wide bandpass).

To collect this data, both the excitation sources front illuminated theblock transversely at oblique angles of between 10 and 20 degrees fromthe plane of the face. No dichroic filter was needed. Emitted light wascollected by a lens with a high numerical aperture, looking normal tothe face of the block. Illumination from two or more transversedirections (e.g. left and right or top and bottom) produced more uniformexcitation and emission patterns.

FIG. 8A shows an image of fluorescence of tissue in the presence ofparaffin using a 365 nm excitation source with an emission filtercentered at 560 nm (55 nm wide bandpass). FIG. 8B shows paraffinfluorescence using a 280 nm excitation source and an emission filtercentered at 405 nm (20 nm wide bandpass). As shown in FIG. 8B, paraffincan undergo fluorescence without appreciable fluorescence of tissue inan embedded sample. The results indicate that contrast between tissueand paraffin may be further enhanced by examining fluorescence in theregion of the paraffin.

In view of this disclosure it is noted that the methods and apparatuscan be implemented in keeping with the present teachings. Further, thevarious components, materials, structures and parameters are included byway of illustration and example only and not in any limiting sense. Inview of this disclosure, the present teachings can be implemented inother applications and components, materials, structures and equipmentto implement these applications can be determined, while remainingwithin the scope of the appended claims.

Exemplary Embodiments

Exemplary embodiments provided in accordance with the presentlydisclosed subject matter include, but are not limited to, the claims andthe following embodiments:

A1. A method of determining the location of a tissue in an embeddedsample, the method comprising:

irradiating an embedded sample with light, wherein the embedded samplecomprises a tissue and an embedding medium;

detecting fluorescence emission of the embedded sample; and

determining the location of at least a portion of the tissue in theembedded sample based on the fluorescence emission.

B1. A method of determining the location of a tissue in an embeddedsample, the method comprising:

irradiating an embedded sample comprising a tissue and an embeddingmedium with at least one light source to produce a first fluorescenceemission and a second fluorescence emission;

detecting the first fluorescence emission and the second fluorescenceemission; and

determining the location of at least a portion of the tissue in theembedded sample based on the first fluorescence emission and the secondfluorescence emission.

B2. The method of embodiment B1, wherein the first fluorescence emissionis a fluorescence emission of the embedding medium.

B3. The method of embodiment B1 or B2, wherein the second fluorescenceemission is a fluorescence emission of a component of the tissue.

B4. The method of any of embodiments B1 to B3, wherein the firstfluorescence emission and/or second fluorescence emission has a maximumat a wavelength of from 300 nm to 600 nm, preferably from 300 nm to 550nm, more preferably from 300 nm to 500 nm, or even more preferably from300 nm to 450 nm.

B5. The method of any of embodiments B1 to B4, wherein the firstfluorescence emission has maximum fluorescence at a wavelength of from a375 nm to 425 nm and the second fluorescence emission has maximumfluorescence a wavelength of from 500 nm to 600 nm.

AB1. The method of any of the preceding embodiments, wherein theembedding medium is a paraffin.

-   -   AB1.a The method of embodiment AB1, wherein the embedded sample        is a formalin-fixed paraffin-embedded (FFPE) tissue block.    -   AB1.b The method of embodiment AB1 or AB1.a, wherein the        paraffin is granulated paraffin wax, fully refined paraffin wax,        semi-refined paraffin wax, or a combination thereof.    -   AB1.c The method of embodiment AB1 or AB1.a, wherein the        paraffin is a blend of fully refined paraffin wax and a        synthetic resin or polymer.    -   AB1.d The method of embodiment AB1 or AB1.a, wherein the        paraffin is Spectrum paraffin, Millipore paraffin, Fisherfinest        Histopath paraffin wax, EMS Paramat, Paraplast & Polyfin, Sakura        Finetek Tissue Tek VIP, Leica Surgipath Paraplast, or a        combination thereof.    -   AB1.e The method of any of embodiments AB1 to AB1.d, wherein the        paraffin comprises dimethylsulfoxide (DMSO).

AB2. The method of any of embodiments A1 to B5, wherein the embeddingmedium is an epoxy resin.

-   -   AB2.a The method of embodiment AB2, wherein the epoxy resin is a        glycidyl epoxy.        -   AB2.a.i The method of embodiment AB2.a, wherein the glycidyl            epoxy resin is glycidyl amine, glycidyl ester, glycidyl            ether, or a combination thereof.        -   AB2.a.ii The method of embodiment AB2.a., wherein the epoxy            resin is Araldite, Quetol, Epon 812, Embed 812, Poly-Bed            812, or a combination thereof.        -   AB2.a.iii The method of embodiment AB2.a, the glycidyl epoxy            resin is ethylene glycol diglycidyl ether.    -   AB2.b The method of embodiment AB2, wherein the epoxy resin is a        non-glycidyl epoxy.        -   AB2.b.i The method of embodiment AB2.b, wherein the            non-glycidyl resin selected from an aliphatic and cyclo            aliphatic resin.

AB3. The method of any of the preceding embodiments, wherein thefluorescence emission is detected using an imaging device.

-   -   AB3.a The method of embodiment AB3, wherein the fluorescence        emission is detected using an imaging device comprising a        camera.    -   AB3.b The method of embodiment AB3.a, wherein the camera is a        digital camera.    -   AB3.c The method of embodiment AB3 to AB3.b, wherein a digital        image of the fluorescence emission is used to determine the        location of the tissue in the embedded sample.

AB4. The method of any of the preceding embodiments, wherein the methodis used to determine the location of a tissue surface.

AB5. The method of any of the preceding embodiments, further comprisingslicing a section from the embedded sample after determining thelocation of the tissue surface.

-   -   AB5.a The method of embodiment AB5, further comprising slicing a        section from the embedded sample and accepting or rejecting the        section based on the determined location of the tissue surface.

AB6. The method of any of the preceding embodiments, wherein theembedding medium exhibits no substantial fluorescence when irradiated.

AB7. The method of any of the preceding embodiments, wherein theembedded sample is irradiated with light having a wavelength of 200 nmto 600 nm, preferably 250 nm to 550 nm, more preferably 300 nm to 550nm, or even more preferably 300 nm to 500 nm.

AB8. The method of any of the preceding embodiments, wherein theembedded sample has a maximum fluorescence emission at a wavelength offrom 300 nm to 600 nm.

AB9. The method of any of the preceding embodiments, wherein thefluorescence emission is generated by autofluorescence of a component ofthe tissue.

-   -   AB9.a The method of embodiment AB9, wherein the component is        collagen, elastin, tryptophan, a porphyrin, a flavin, NADH,        pyridoxin, a lipo-pigment, or a combination thereof.    -   AB9.b The method of embodiment AB9, wherein the component has a        maximum fluorescence emission at a wavelength of from 300 nm to        550 nm.

AB10. The method of any of the preceding embodiments, wherein theirradiating is performed multiple times and wherein the embedded sampleis cut prior to each irradiation.

AB11. The method of any of the preceding embodiments, wherein the tissueis a human tissue.

AB12. The method of any of the preceding embodiments, wherein the tissueis an animal tissue.

-   -   AB12.a The method of embodiment AB12, wherein the tissue is a        mouse, rat, dog, or primate tissue.

AB13. The method of any of the preceding embodiments, wherein the tissueis from an organ or anatomical part.

-   -   AB13.a The method of any of the preceding embodiments, wherein        the tissue is isolated from the breast, prostate, lung, colon,        rectum, urinary bladder, uterine corpus, thyroid, kidney, oral        cavity (e.g., tonsil), pancreas, liver, cervix, stomach, small        intestine, brain, spinal cord, heart, bone, joints, esophogus,        gallbladder, adipose, skin, spleen, placenta, penis, urethra,        fallopian tube, ovary, vulva, adrenal glands, appendix, or eye.

AB14. The method of any of the preceding embodiments, wherein the tissueis pelleted cells from a human or an animal source.

AB15. The method of any of the preceding embodiments, wherein the tissueis diseased or healthy tissue.

AB16. The method of any of the preceding embodiments, wherein the tissueis used to identify cancer, infectious disease, metabolic disease,degenerative disease, inflammatory disease, or a combination thereof.

AB17. The method of any of the preceding embodiments, wherein thepresent methods are performed to locate an embedded tissue for use in afluorescence in situ hybridization (FISH) testing method.

AB18. The method of any of the preceding embodiments, wherein thepresent methods are performed to locate an embedded tissue for use in achromogenic in situ hybridization (CISH) testing method.

AB19. The method of any of the preceding embodiments, wherein theautofluorescence of one or more endogenous species is measuredquantitatively to determine the location of tissue in the embeddedsample.

AB20. The method of any of the preceding embodiments, wherein pixelintensity of a digital image is used to determine the location of thetissue in the embedded sample.

AB21. The method of any of the preceding embodiments, wherein the methodcomprises sectioning or trimming the embedded sample.

-   -   AB21.a. The method of any of the preceding embodiments, wherein        the method comprises staining a tissue section with at least one        stain, wherein the tissue section is obtained by sectioning or        trimming the embedded sample.

AB22. The method of any of the preceding embodiments, wherein theembedding medium comprises a fluorescent dye.

AB23. The method of any of the preceding embodiments, wherein theembedded sample is irradiated by two or more light sources.

AB24. The method of any of the preceding embodiments, wherein theembedded sample is irradiated using a light source selected from alight-emitting diode, mercury arc lamp, xenon arc lamp, LASER, and acombination thereof.

AB25. The method of any of the preceding embodiments, wherein the methodcomprises front illuminating the embedded sample transversely.

AB25.a The method of embodiment AB25, wherein the embedded sample isfront-illuminated at an oblique angle of from about 10 degrees to about20 degrees from a plane of a face of the embedded sample.

C1. An apparatus for slicing a tissue section from an embedded sample,the apparatus comprising:

a microtome comprising a sample holder adapted for linear motion, aknife holder and a knife held by the knife holder opposite the sampleholder, such that when the sample holder is moved linearly, a sampleheld by the sample holder is sliced by the knife to form a tissuesection;

at least one light source directed at the sample holder; and

an optical system positioned to capture emitted light from a sample heldby the sample holder.

C2. The apparatus of embodiment C1, wherein the optical system comprisesa camera.

-   -   C2.a The apparatus of embodiment C2, wherein the camera is a        digital camera.    -   C2.b The apparatus of embodiment C2 or C2.a, wherein the camera        is a multicolor camera having microfilters in front of each        pixel.

C3. The apparatus of embodiment C1, further comprising a processor incommunication with the optical system and configured to provide a signalbased on a fluorescence emission from the sample.

C4. The apparatus of embodiment C1 to C3, the at least one light sourceis an LED light source, a mercury arc lamp, a Xenon arc lamp, or aLASER.

C5. The apparatus of embodiment C1 to C4, the optical system comprisesat least two light sources, at least three light sources, or at leastfour light sources.

C6. The apparatus of embodiment C1 to C5, wherein the apparatuscomprises a filter cube with a dichroic beam splitter with excitationand emission filters.

-   -   C6.a The apparatus of embodiment C6, wherein the apparatus        comprises an additional lens after the dichroic filter to focus        the emitted light onto an imaging sensor.

C7. The apparatus of embodiment C1 to C6.a, wherein the apparatuscomprises an emission filter in a filter cube assembly, where switchingof at least one excitation source switches at least one filter.

C8. The apparatus of embodiment C1 to C7, wherein the apparatus includesone or more excitation filters.

C9. The apparatus of embodiment C1 to C8, wherein the apparatuscomprises an aperture.

-   -   C9.a The apparatus of embodiment C9, wherein the aperture is a        high numerical aperture.

C10. The apparatus of embodiment C1 to C9.a, the apparatus comprises oneor more emission filters.

C11. The apparatus of embodiment C1 to C10, wherein the apparatuscomprises an imaging lens.

C12. The apparatus of embodiment C1 to C4, wherein the apparatuscomprises a microtome blade, at least one light source, at least oneexcitation filter, at least one aperture, at least one emission filter,a lens assembly, and at least one camera.

C13. The apparatus of embodiment C1 to C4, wherein the apparatuscomprises a microtome blade, at least two light sources, at least twoexcitation filters, at least one aperture, at least two emissionfilters, a lens assembly, at least one camera, and at least onemechanism for switching between emission filters.

C14. The apparatus of embodiment C1 to C4, wherein the apparatuscomprises a microtome blade, at least two light sources, at least twoexcitation filters, at least one aperture, a dual-band bandpass emissionfilter, a lens assembly, and at least one multi-color camera.

-   -   C14.a The apparatus of embodiment C14, wherein the multicolor        camera has microfilters in front of each pixel.

C15. The apparatus of embodiment C1 to C4, wherein the apparatuscomprises a microtome blade, at least one light source, at least oneexcitation filter, at least one aperture, an objective lens assembly, atube lens or relay lens, a dichroic beamsplitter, at least one emissionfilter in filter cube assembly, and at least one camera.

We claim:
 1. A method of determining the location of a tissue in anembedded sample, the method comprising: irradiating an embedded samplewith light having a wavelength of from about 200 nm to about 600 nm,wherein the embedded sample comprises a tissue and an embedding medium;detecting fluorescence emission of the embedded sample; and determiningthe location of at least a portion of the tissue in the embedded samplebased on the fluorescence emission.
 2. The method of claim 1, whereinthe embedding medium is a paraffin.
 3. The method of claim 1, whereinthe embedded sample is a formalin-fixed paraffin-embedded (FFPE) tissueblock.
 4. The method of claim 1, wherein the fluorescence emission isdetected using an imaging device comprising a camera.
 5. The method ofclaim 4, wherein a digital image of the fluorescence emission is used todetermine the location of the tissue in the embedded sample.
 6. Themethod of claim 5, wherein pixel intensity of the digital image is usedto determine the location of the tissue in the embedded sample.
 7. Themethod of claim 1, wherein the method is used to determine the locationof a tissue surface.
 8. The method of claim 7, further comprisingslicing or trimming a section from the embedded sample after determiningthe location of the tissue surface.
 9. The method of claim 8, whereinthe method comprises staining the tissue section with at least onestain.
 10. The method of claim 1, wherein the light has a wavelength offrom about 250 nm to about 450 nm.
 11. The method of claim 1, whereinthe fluorescence emission is generated by autofluorescence of acomponent of the tissue.
 12. The method of claim 11, wherein thecomponent is elastin or collagen.
 13. A method of determining thelocation of a tissue in an embedded sample, the method comprising:irradiating an embedded sample comprising a tissue and an embeddingmedium with at least one light source to produce a first fluorescenceemission and a second fluorescence emission; detecting the firstfluorescence emission and the second fluorescence emission; anddetermining the location of at least a portion of the tissue in theembedded sample based on the first fluorescence emission and the secondfluorescence emission.
 14. The method of claim 13, wherein the embeddedsample is irradiated by at least two light sources.
 15. The method ofclaim 13, wherein the embedded sample is a formalin-fixedparaffin-embedded (FFPE) tissue block and the first fluorescenceemission occurs via fluorescence of paraffin.
 16. The method of claim13, wherein the method comprises front illuminating the embedded sampletraversely.
 17. The method of claim 13, wherein the embedded sample isfront-illuminated at an oblique angle of from about 10 degrees to about20 degrees from a plane of a face of the embedded sample.
 18. Anapparatus for slicing a tissue section from an embedded sample, theapparatus comprising: a microtome comprising a sample holder adapted forlinear motion, a knife holder and a knife held by the knife holderopposite the sample holder, such that when the sample holder is movedlinearly, a sample held by the sample holder is sliced by the knife toform a tissue section; at least one light source directed at the sampleholder; and an optical system positioned to capture emitted light from asample held by the sample holder.
 19. The apparatus of claim 18, whereinthe optical system comprises a camera.
 20. The apparatus of claim 18,further comprising a processor in communication with the optical systemand configured to provide a signal based on a fluorescence emission fromthe sample.